Wednesday, April 30, 2014

HL-60 cells are human promyelocytic leukemia cells that were originally obtained from a woman with leukemia. They are valuable biomedical tools that are used in many studies. But really, doesn't everyone want to know how fast they can go? In particular, could they beat Dictyostelium (amoebic slime mold) cells in a race?

Dictyostelium

Inquiring minds want to know. At least, the inquiring minds behind the first World Dicty Race want to know. They're encouraging labs to submit to submit their fastest cells for a show down.

Tuesday, April 29, 2014

The most common method for keeping swimming pools free of microbial pathogens is to add chlorine. Unfortunately, the chlorine in the water can combine with other molecules to form harmful byproducts like trichloramine (NCl3) and cyanogen chloride (CNCl). Researchers from China Agricultural University and from Purdue University found that this is particularly apt to happen when the chlorine is combined with uric acid.

Now, before you jump to conclusions, I should say that uric acid is present in human sweat. In really tiny amounts. There’s nearly 400 times more uric acid in urine than in sweat. So, I guess go ahead and jump to that conclusion because according to the authors, about 93% of the uric acid in swimming pools comes from pee.

How bad could it be? Well, NCl3 has been associated with severe lung injury. CNCl can affect the heart, lungs and central nervous system.

Bottom line: don’t pee in the pool. Even if you’re an olympic swimmer.

Monday, April 28, 2014

We know that all human beings (Homo sapiens sapiens) can trace their origins back to Africa. Sometime between 100 and 200 thousand years ago (ka) the first of these modern humans migrated out of Africa and spread across the rest of the globe. One line of evidence for this is that the further you go from sub-Saharan Africa, the more similar people are genetically.

Think about this way: let’s say there are ten different people living in Africa. One of them leaves. Over the next 100 ka, his descendants settle throughout Asia, but they all still share the common ancestor that left Africa. The descendants of the nine people who remained in Africa have no such commonality. Their shared ancestor dates from the evolution of the human species far earlier. Therefore, the people living in Africa today are far more diverse genetically than any of the groups living elsewhere in the world.

So far so good. What isn’t clear is whether the dispersal from Africa occurred as a single event or multiple events at different times in history. And what route did those groups of people use as they traveled around the world? Hugo Reyes-Centeno of Eberhard Karls University of Tübingen and his colleagues used both genetics and cranial features to compare four possibilities: a single dispersal with a northern route, a single dispersal with a southern route, multiple dispersals using both routes, and multiple dispersals using both routes, but where groups of people became stranded and thus genetically isolated along the way.

They conclude that the most likely scenario is the last one. Around 130 ka, humans began traveling across Southern Asia. A separate diaspora occurred about 50 ka taking humans into Europe.

Thursday, April 24, 2014

If you’ve flown large distances, chances are you’ve experienced jet lag. This condition occurs when a person’s internal clock does not align with the environment. Until the traveler readjusts his circadian rhythm, he may not be hungry when it’s time to eat or sleepy when it’s time to sleep. But it’s not just travelers who are affected by jet lag. Shift workers too must adjust to being productive at times when their bodies think it’s time to sleep.

Needless to say, it can be quite disruptive to live this way for long. For most people, readjusting, or ‘entrainment’ takes about one day per hour shifted. The recovery process can be sped up by exposure to bright light, but only if that exposure occurs at the right times. So, how does one know what those times are? Wouldn’t it be great if there were an app for that?

Enter Kirill Serkh of Yale University and Daniel Forger from the University of Michigan. They created a mathematical model for optimally scheduling anti-jet lag light periods. Then Olivia Walch made it an app:

To follow the apps recommendations, a person should experience one block of light and one block of darkness per day (and they should be very bright and very dim respectively) starting and ending at specified hours. For example, the app might tell the person to turn on the lights at 5:00 am and turn them off 7:20 pm. If you follow the recommendations, you should be able to knock a couple of days off your recovery time.

Tuesday, April 22, 2014

In collaboration with the BioVisions program at Harvard, Xvivo Scientific Animation has created some amazing animations of the insides of cells. The first one was made in 2006 and entitled The Inner Life of the Cell.You can watch DNA and RNA zipping and unzipping and proteins busily going about their business in their internal metropolis. Now there's a new video (Inner Life of a Cell/ Protein Packing) which gives people a better idea of just how crowded it is within a cell: In both videos, the oddly shaped clumpy objects are proteins. Here's one shot from the second animation, showing a variety of proteins in close contact, just as they are in real life:

Monday, April 21, 2014

Do you get irritable when you’re hungry? Do you tend to take out that aggression on your loved ones? If so, you’re in good company. Brad Bushman of The Ohio State University and his colleagues found that when people have low glucose levels, they like to stick pins in dolls representing their spouses.

The researchers measured the glucose levels of 107 couples twice a day (before breakfast and late evening) for three weeks. Every evening, participants were given voodoo dolls and told to stick 0 to 51 pins into them to demonstrate how much anger they felt towards their spouses. The pin-sticking was done alone without the spouse being present.

At the end of the 21 days, each person participated in a button-pressing game. Whoever pressed the button first was given the privilege of blasting the loser with some really unpleasant sounds (think dentist drills and chalkboard squeaks). The winner could pick both the decibel level and the duration of the sound blast, including no blast at all.

The participants thought they were competing with their spouses, who were not visible during the test. In reality, they were competing with a computer that made sure they lost 13 out of 25 trials and that they received a random sampling of the noise options.

The researchers found that when they accounted (as best they could) for marital and sexual satisfaction and for typical levels of aggression (some couples were routinely more aggressive toward each other than others), daily evening glucose levels did correlate with number of pins stuck in the voodoo dolls. In case you’re wondering, women tended to stick more pins than men.

In the noise-blast test, people with lower average evening glucose levels blasted what they thought were their spouses with louder and longer noise bursts.

There are a lot of possible things besides just low glucose levels that can make a person want to stick pins in his spouse or blast her with unpleasant noises. However, between other trials showing that people have less impulse control when they have low glucose levels and my own personal experiments with hunger and irritability, I find these results totally believable.

Thursday, April 17, 2014

Why do zebras have those flashy stripes? In a
world where predators could be lurking anywhere, being so boldly
conspicuous seems like a huge handicap. There must be some kind of
evolutionary advantage to that distinctive coloring and biologists have
come up with several ideas. The stripes might be courtship or other
social cues, helping the animals mate or bond in groups. They might
allow the animals to identify each other. They might confuse predators
by making the zebras blend together. Perhaps they offer some type of
temperature control. Nope. Tim Caro of the University of California, Davis and his colleagues ruled out those possibilities. It turns out that it’s all about the bugs.

That’s right, bugs. More specifically, biting insects like tsetse flies, stomoxys stable flies and tabanid biting flies. The researchers found that the ranges of animals with body stripes (zebras) exactly matched the ranges of these bloodsucking insects.

In the diagram below, you can see the different species of wild equine. Some have full body stripes, some leg stripes, some neck stripes and some are not striped at all. The blue dots show species not plagued by tabanid flies. Notice that those are the animals with no stripes. There was no such correlation with other factors like the presence of certain predators or temperature.

But aren't there plenty of other animals living in those same areas that are not striped? Yes, but zebras are covered with short hairs that biting insects can penetrate with their mouth parts. Non-striped mammals living in the same areas typically have longer, thicker fur that the flies can't get through.How do stripes help animals avoid biting insects? Apparently, many insects, including tabanids and tsetses, don’t like to land on striped surfaces. And indeed, solid colored feral horses suffer much more harassment from flies than do their striped cousins.

The idea that insect parasites drove the evolution of stripes isn’t settled science yet, but it’s a fascinating hypothesis. I can’t wait to see if further studies confirm it.

Tuesday, April 15, 2014

The Kuiper asteroid belt is full of objects that orbit the sun out beyond Neptune. Some of these objects have orbits that cross the paths of the gas giants, but they don’t generally get any closer than that.

This means that most of these objects are too far away for us to ever learn much about them if we can even detect them in the first place. But sometimes we get lucky. If one of these objects passes in front of (and consequently dims the light) of another star, we can use that information to determine how big the object is.

When astronomers observed an asteroid named Chariklo passing in front of a star (not the sun) last summer, they were able to calculate not only its size (250 kilometers in diameter), but something far more amazing. They found that Chariklo has rings. To be exact, it has two rings, one thin one and one thicker one. This makes the asteroid only the fifth object in our solar system to have rings, after Jupiter, Saturn, Uranus and Neptune.

How did the cosmologists come this conclusion? As Chariklo traveled across the path of that distant star, the light from that star was dimmed. But that slight fading didn’t happen just once, as it would if a single body were crossing in front of the star. Instead, there were five light dips: a small one (A), a bigger one (B), a much bigger one (C), then one exactly the same size as B, and finally one the exact same size as A. The regularity of the dips strongly suggests that A and B are rings.

It’s very likely that Chariklo is not the only asteroid with rings. After all, we once thought Saturn was the only planet with rings, and we now know that all the gas giants have them. It may be all the more amazing if relatively tiny asteroids can have rings since none of the rocky planets, which are far larger than asteroids, have rings. Even Mercury is nearly 20 times larger than Chariklo and it doesn't have rings.

Monday, April 14, 2014

If you live in North America, you're going to have a chance to see a lunar eclipse tonight.

A lunar eclipse occurs when the moon passes through Earth's shadow. Phil Plait has an excellent description of this upcoming event over at Bad Astronomy, including this helpful diagram:

Note: objects are not to scale. Drawing by Shutterstock / fluidworkshop

You can also see an explanation of how the eclipse will effect the Lunar Reconnaissance Orbiter (LRO), which is currently orbiting the moon, below:When is the best viewing? The main event should take place between about 2- 5 am EDT. Plan accordingly.

Friday, April 11, 2014

The superiority of Old Italian violins like those made by Stradivari is legendary. For hundreds of years, people have tried to discover the source of that excellence. Was it the varnish? A property of the wood? The surprising answer may be that it's a trick question. Those old violins may not actually be any better than new violins. So say renowned violin soloists during blinded tests.

Claudia Fritz of Sorbonne Universités and her colleagues invited ten multiple award winning violin soloists to participate in their study. All of the musicians had experience playing Old Italian violins and some used them exclusively. While wearing welder’s goggles that made it impossible to identify violins by sight, the violinists were presented with six new violins (no more than two decades old, but antiqued to have the same worn edges as much older violins) and six old violins (made by 17th and 18th century masters like Guarneri del Gesu and Stradivari).

After playing their own violin as a reference, the subjects tried out the twelve violins and ranked them for preference, as if they were considering buying them. Once he had selected his four highest rated violins, each musician was presented with three violins: his own, his top pick out of the twelve, and his top pick from the opposite category. For example, if he liked an old violin the most, the third violin would be his top ranked new violin. Those three violins were then rated for a variety of musical attributes such as tone quality and projection.

The entire experiment was repeated twice, first in the practice room within the home of professional musicians and later in a 300 seat concert hall.

The two highest scoring violins were both new ones. Four of the six violins that had been ranked number one by at least one musician were new ones. All but one new violin was at least one person’s top pick, whereas four of the six old violins were no one’s top choice. For most criteria, the violinists preferred a top ranked new violin to their own violin. In contrast, they tended to prefer the qualities of their own violins to those of old violins.

No one is suggesting that the old Italian violin makers did not create masterpieces. It’s just that those instruments may not be as magical as they are given credit for. It also means that our modern violin manufacturers are doing an excellent job.

Thursday, April 10, 2014

If you wanted to study meteorological conditions before the advent of modern recording devices, what would you do? Well, if you’re like Christos Zerefos of the Academy of Athens or his colleagues, you’d look at old paintings. The researchers used paintings of sunsets made from the year 1500 to 2000 to estimate the amount of pollution in the air at those times.

First off, you may be wondering what could have produced enough pollution to blot the sky hundreds of years before the industrial revolution. The answer is volcanic eruption. Sure enough, paintings made within a few years of major eruptions have redder skies than paintings made at other times. This is because the ash and dust in the air after an eruption scatter the sunlight, shifting the ratio of red to green light.

To test how accurately a painting could be in predicting the clarity of the atmosphere, the researchers asked Panayiotis Tetsis, a colorist and landscape artist, to paint a series of sunset pictures from the island of Hydra. Unbeknownst to Tetsis, during the experiment there happened to be a Saharan dust storm blowing over Greece. You can see the results below:

Greek landscape painter Panayiotis Tetsis created the top images on June 19 and 20, 2010, respectively. The photographs below them reflect the real sunsets on those evenings. There were more aerosols in the sky, and more red in Tetsis' painting, on June 19.
P. Tetsis (paintings) and C. Zerefos (photos).

The top two panels are of Tetsis’ paintings, the bottom panels are photographs taken while he was painting. The panels on the left were made during the dust storm, the panels on the right were made the next day. Notice how much redder the sky is during the dust storm in both the photographs and the paintings.

If earlier artists were equally good at capturing color differences, then paintings made hundreds of years ago could be useful for determining pollution levels.

Wednesday, April 9, 2014

Drummer Jason Barnes lost his right arm after being electrocuted two years ago. Thanks to help from Gil Weinberg’s lab at Georgia Tech, Barnes now has a robotic arm with which to make music.

Notice that the prosthesis holds two drumsticks, only one of which is controlled by Barnes’ bicep muscles. The second drumstick is an independent robotic device that can improvise, based on what Barnes is doing with the drumsticks he controls.

Tuesday, April 8, 2014

A group of physics students from the University of Leicester calculated whether someone could defy speed cameras by outrunning them. The good news is that it is definitely possible. The bad news is that he’d have to be traveling at 119 million miles per hour.The students based their calculations on what it would take to create a sufficient Doppler effect to blur the images taken by a camera. The Doppler effect is the change in frequency of waves as the object emitting those waves first approaches and then passes the observer. You can notice this yourself in the changing sound of a siren as an emergency vehicle catches up with you and then passes you. The sound waves between you and the vehicle ‘bunch up’ as the distance closes, resulting in a higher pitched siren. As the vehicle moves away from you, the sound waves stretch out.

In light, objects moving away from an observer are shifted toward the red end of the spectrum. The faster the object, the bigger the shift. Because speed cameras take pictures of fleeing cars, the students worked out how fast a car would need to travel to create a redshift great enough to make the license plate undetectable. The answer: about a sixth of the speed of light.

I feel a couple of caveats are in order. If you’re a fan of the show Mythbusters, then you know that Jamie Hyneman and Adam Savage also tried to outrun speed cameras and were able to do so by going about 200 miles per hour. This is obviously considerably less than a hundred million miles per hour. One possible reason for the discrepancy is that the University of Leicester students ignored camera speed. If a camera has a shutter speed of 1/1000 of a second, a car traveling 200 miles per hour would have moved about three feet during the time it took the camera to snap the image. I’m not sure what the shutter speed or focal range is for traffic cameras, but it’s not hard to see how the world’s fastest cars could defeat them.

One more thing to note: this study was conducted in the United Kingdom, where license plates are typically yellow. The exact speed required to create enough of a doppler shift to fool the cameras will vary slightly with different plates.

Monday, April 7, 2014

Take a look at the pictures below. One of them is an expression of real pain and the other is faked. Which one do you think is real?

Credit: Image courtesy of University of California - San Diego

I’ll reveal the answer a little later. But for now, would it surprise you to know that most people are no better than chance at distinguishing actual pain from simulated pain? Even after training, human observers were only 55% accurate in picking out who was only faking. Computers, on the other hand, have no such limitations and could distinguish genuine from faked expressions 85% of the time.

Scientists led by Marian Bartlett of the University of California, San Diego and Kang Lee of the University of Toronto compared human observers with a computer vision system called CERT (Computer Expression Recognition Toolbox). CERT detects human faces and codes the positions and actions of facial muscles using a program called FACS (Facial Action Coding System). FACS scores incremental movements in individual facial muscles.

The models for the experiment were asked to place their hands in either ice water (pain) or warm water (fake) for one minute. Their facial expressions were recorded and played back for either the human observers or the CERT program. As mentioned, the humans were pretty much guessing whereas the computer was actually quite good at spotting the fakers.

I’m not sure how CERT’s pain-detecting abilities would be used in the real world. I’m envisioning mothers saying: “So, you can’t go to school because you have a stomach ache? We’ll see about that.”

Now for the answer. If, like me, you guessed that image B on the right was fake, you’re wrong. Image B shows the expression of real pain. It’s image A that’s fake.

Friday, April 4, 2014

We sometimes think of cancer as a disease of modern life, both because it can be caused by modern living conditions (smoking, pollution) and because it doesn’t usually manifest until later in life. If most of a population dies at a young age, they will probably never get cancer. Add this to the fact that it’s difficult to find archeological evidence of specific diseases and you have scant evidence for the early appearance of cancer.

That doesn’t mean that cancer wasn’t around. Scientists from Durham University and from the British Museum have found the remains of one young man who lived over three thousand years ago who almost certainly had cancer.

The man had lived in what is now Sudan and was most likely 25-35 years old when he died. As you can see in the graphic below, much of his skeleton was affected by cancerous lesions.

By the way, this unfortunate individual is not the earliest example of cancer. A 6000 year old skeleton in Austria was discovered with signs of multiple myeloma. There have also been about 50 cancerous individuals described from ancient Egypt, a region that excelled both in body preservation and in record keeping.

Thursday, April 3, 2014

Worldwide, colorectal cancer is one of the most commonly diagnosed forms of cancer. In the U.S., it is the second leading cause of cancer-related deaths (behind only lung cancer), and kills about 50,000 people per year. Luckily, there is a screening test that can catch the disease early enough to treat it. Even better, that test could just get a whole lot less invasive.

The standard test for colon cancer is called colonoscopy. Not to put too fine a point on it, a long flexible tube containing a camera is passed through the anus into the large intestines. The entire colon is carefully examined for lesions or polyps, which are removed for biopsy. The test requires the complete emptying of the bowels prior to the procedure, which is generally agreed upon to be unpleasant.

Perhaps for this reason, nearly half of eligible patients avoid colon cancer screenings. Thanks to researchers from the Mayo Clinic, there may soon be an alternative. In partnership with Exact Sciences, the scientists have developed a new screening tool called Cologuard.

Cologuard tests stool samples for DNA changes associated with colon cancer. In the past, such tests were not sensitive enough to replace colonoscopy. However, new techniques in DNA detection and sequencing have made Cologuard a promising option.

The researchers recruited about 10,000 people between the ages of 50 and 84 for their study. Each person provided a stool sample (no cleansing, dieting, or medication required) and subsequently underwent colonoscopy (with the usual cleansing).

By colonoscopy, 65 patients were found to have cancer. The DNA testing Cologuard identified 60 of them. That’s a pretty good success rate, and certainly better than other noninvasive tests.

Obviously, there is room for improvement, especially if Cologuard is meant to completely replace colonoscopy. However, if you consider that this test might get many more people screened, Cologuard could be an extremely useful tool in an oncologist’s arsenal.

Wednesday, April 2, 2014

Cornell University students Ray Li and Michael Ndubuisi have created a new way to make music. Their instrument is called the 'Aura' and relies on the movement of sensors across a magnetic field. That's description doesn't do it justice though. It's more like something you'd see on The Sorcerer's Apprentice.

Tuesday, April 1, 2014

If animals played April Fool's jokes on each other, it would be by using mimicry and camouflage.

One of the great masters of tricking other animals is the Indonesian mimic octopus:

Camouflage is widespread in the animal kingdom, but here's one I particularly like: the pygmy seahorse.The tiny creatures (no more than an inch long when fully stretched) were first discovered by scientists examining some coral they had in their laboratory. Imagine their surprise!

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.